User: jevanveen

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jevanveen20
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j********@alum.mit.edu

Posts by jevanveen

<prev • 16 results • page 1 of 2 • next >
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Answer: A: Single cell DEG analysis. Wildly different results from different FindMarkers te
... I partly figured this out and thought I would update in case someone else comes looking with the same issue. It seems that I was getting crazy LogFC's and weird looking volcanoes because of a problem with the normalization of my data. For these analyses I had used the Seurat "SCT integration" pipe ...
written 3 months ago by jevanveen20
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Comment: C: Single cell DEG analysis. Wildly different results from different FindMarkers te
... Sorry Igor, you are of course correct that the "data" slot is log normalized, and NOT scaled. But when I do it the correct way, using the normalized data slot, things look wrong. When I use counts, which is only recommended for tests like negbinom or DESeq2, the results look much more correct, irr ...
written 3 months ago by jevanveen20
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Comment: C: Single cell DEG analysis. Wildly different results from different FindMarkers te
... Right you are! Commands that will give data producing the first plot: FindMarkers(all.cells.integrated, ident.1 = "Neuron_LowEarthOrbit", ident.2 = "Neuron_Underwater", test.use = "wilcox") FindMarkers(all.cells.integrated, ident.1 = "Neuron_LowEarthOrbit", ident.2 = "Neuron_Underwater", t ...
written 3 months ago by jevanveen20 • updated 3 months ago by genomax92k
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Single cell DEG analysis. Wildly different results from different FindMarkers test
... Hello and thank you in advance for your help. I am doing a single cell RNA seq experiment and analyzing data with Seurat. I have four treatment groups, which I integrated, then identified clusters of different types of cells in the brain. Everything looked exactly right at this point. Then I wante ...
rna-seq seurat written 3 months ago by jevanveen20
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Comment: C: Looking for perspective on a odd MA plot / skewed data
... This is helpful information... I have a decent amount of experience with R, but I did my first seq analyses on galaxy, and so... if it aint broke, don't fix it, right? Well, I guess now it's broke, lol. Will give it a shot. Cheers ...
written 10 months ago by jevanveen20
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Comment: C: Looking for perspective on a odd MA plot / skewed data
... Thanks for responding! Replicates are 3 in one condition, 4 in the other. Sorry, do you mean MA-plot with non-shrunken LFC values? I am still running my alignments and DESeq on usegalaxy. As far as I can tell, the LFC values are not shrunken by default. ...
written 10 months ago by jevanveen20
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Looking for perspective on a odd MA plot / skewed data
... Hello Biostars! I (and collaborators) recently performed a patch-seq experiment... That is, we did patch-clamp recording of neuronal firing, then aspirated the contents of recorded cells, and made RNA seq compatible libraries. Data look alright - certainly there is a lot of PCR duplication. Pro ...
patch-seq rna-seq written 10 months ago by jevanveen20 • updated 9 months ago by Biostar ♦♦ 20
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Comment: C: Bonferroni multiple corrections question
... This is fantastically helpful and straight to the point. Thank you very much!!! ...
written 13 months ago by jevanveen20
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Bonferroni multiple corrections question
... Hello Biostars! I have been analyzing some single cell RNA sequencing data, which compares neural transcriptomes from mice treated with either vehicle, or a drug. All the basic stuff is going fine. When I get my clusters, I find not many *super* interesting significant drug induced DEGs. If I do ...
scrna-seq rna-seq gsea statistics written 13 months ago by jevanveen20 • updated 13 months ago by dsull1.7k
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Comment: C: Single cell RNA-seq guided correlation analysis
... Hey I know much time has passed, but I went with your suggestion #1, it looked great, and now it is part of my published work: https://elifesciences.org/articles/43668 so thank you very much again! Ed ...
written 13 months ago by jevanveen20

Latest awards to jevanveen

Scholar 3 months ago, created an answer that has been accepted. For A: Single cell DEG analysis. Wildly different results from different FindMarkers te
Popular Question 10 months ago, created a question with more than 1,000 views. For Single cell RNA-seq guided correlation analysis
Popular Question 2.2 years ago, created a question with more than 1,000 views. For Single cell RNA-seq guided correlation analysis

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